One of the current challenges facing biologists is the discovery of novel functional elements in noncoding genomic sequence. With the rapidly increasing number of genomes being sequenced, a comparative genomics approach called ‘phylogenetic footprinting’ has become a favored method for such discovery. The idea underlying phylogenetic footprinting is that selective pressure causes functional elements to evolve at a slower rate than the nonfunctional surrounding sequence. Therefore the most conserved motifs in a collection of homologous regions are excellent candidates as functional elements.
Generates an evolutionary gene print (EvoP) of invariant DNA sequences as they appear in the reference DNA. EVOPRINTER superimposes multiple alignment readouts of individual reference-DNA versus test-genome alignments to proceed. It permits users to find multispecies-conserved sequences (MCSs) that are shared among three or more orthologous DNAs. This tool can be useful to understand gene regulation in all animals.
Assists in discovering phylogenetic footprinting of novel cis-regulatory elements in prokaryotic genomes. MicroFootPrinter provides microbiologists with a convenient front end for FootPrinter, whereby specification of only the species and gene of interest is sufficient for the extraction of all the data necessary for phylogenetic footprinting on that gene. It gives users an automatic and full access to more of 300 prokaryotic genomes.
Analyzes flanking sequences of intergenic miRNAs for Drosophila and 12 fly species. mircisreg performs a two-step phylogenetic footprinting strategy that takes advantages of high sensitivity of motif-detection methods. It also reduces false-positive rate by rough localization of orthologous sequences through pairwise alignments. This method was used to identify a number of putative miRNA gene cis-regulatory elements.
Analyses the temporal component of substitutions. Vestige can combine the temporal and spatial partitioning to highlight processes that may have occurred in a restricted region and stopped millions of years ago or continue to occur in current populations. It delivers functions for foot-printing of length, transition/transversion ratio, and Ka/Ks ratios. This tool simplifies the display of results from the rich probabilistic models of molecular evolution.
Allows users to execute phylogenetic foot-printing on multiple numbers of sequences. BigFoot is based on a Markov chain Monte Carlo (MCMC) approach which inspects both sequence alignments and location of slowly evolving regions. It ensures that alignment error or ambiguity don’t force the detection of slowly evolving regions. Users can shift location of existing boundaries, delete an existing pair or create a new pair of boundaries.